/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.genotyper;

import htsjdk.variant.variantcontext.VariantContext;

/**
 * Author: wbc
 */
public class VariantCallContext extends VariantContext {

    // Was the site called confidently, either reference or variant?
    public boolean confidentlyCalled = false;

    // Should this site be emitted?
    public boolean shouldEmit = true;

    VariantCallContext(VariantContext vc, boolean confidentlyCalledP) {
        super(vc);
        this.confidentlyCalled = confidentlyCalledP;
    }

    VariantCallContext(VariantContext vc, boolean confidentlyCalledP, boolean shouldEmit) {
        super(vc);
        this.confidentlyCalled = confidentlyCalledP;
        this.shouldEmit = shouldEmit;
    }

    /* these methods are only implemented for GENOTYPE_GIVEN_ALLELES MODE */
    //todo -- expand these methods to all modes

    /**
     *
     * @param callConfidenceThreshold the Unified Argument Collection STANDARD_CONFIDENCE_FOR_CALLING
     * @return true if call was confidently ref
     */
    public boolean isCalledRef(double callConfidenceThreshold) {
        return (confidentlyCalled && (getPhredScaledQual() < callConfidenceThreshold));
    }

    /**
     *
     * @param callConfidenceThreshold the Unified Argument Collection STANDARD_CONFIDENCE_FOR_CALLING
     * @return true if call was confidently alt
     */
    public boolean isCalledAlt(double callConfidenceThreshold) {
        return (confidentlyCalled && (getPhredScaledQual() > callConfidenceThreshold));
    }


}
